Chromosome-Level Genome Assembly of the Green Peafowl (<i>Pavo muticus</i>)

Zhang, Mengjie; Lin, Chuyu; Li, Haimeng; Liu, Sixia; Wang, Qing; Yang, Shangchen; Shi, Minhui; Sahu, Sunil Kumar; Zhu, Yixin; Wang, Jiangang; Huang, Junxuan; Hu, Yiyin; Yu, Jieyao; Zhang, Shaofang; Guang-long, LI; Guan, Wenyuan; Lu, Haorong; Xu, Yanchun

doi:10.1093/gbe/evac015

Cited by 10 publications

(27 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The scaffold-level genome of blue peafowl was assembled into pseudochromosomes by mapping onto green peafowl chromosome-level assembly [18] via genome-wide synteny alignment using Chromosemble in Satsuma v2 [41,42].…”

Section: Methodsmentioning

confidence: 99%

“…Pseudochromosome-level assembly of blue peafowl was used to identify the intra-species, and interspecies (between blue and green peafowl) collinear blocks. Collinear blocks for these peafowl species were identified using intra-species and inter-species All-versus-All BLASTP alignments (e-value 10 −5 ) using green peafowl protein sequences obtained from a previous study [18], and protein sequences of blue peafowl obtained from this study. MCScanX [56] was used to perform this analysis with the parameter of five genes required to identify a collinear block [57].…”

Section: Methodsmentioning

confidence: 99%

“…Protein sequences of blue peafowl obtained in this study, green peafowl obtained from a previous study [18], and 49 other avian species available on Ensembl genome browser 105 were used to determine the phylogenetic position of the peafowl species across 12 phylogenetic orders.…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl

Chakraborty

Mondal

Mahajan

et al. 2023

Preprint

View full text Add to dashboard Cite

An intriguing example of differential adaptability is the case of two Asian peafowl species,Pavo cristatus(blue peafowl) andPavo muticus(green peafowl), where the former has a ″Least Concern″ conservation status and the latter is an ″Endangered″ species. To understand the genetic basis of this differential adaptability of the two peafowl species, a comparative analysis of these species is much needed to gain the genomic and evolutionary insights. Thus, we constructed a high-quality genome assembly of blue peafowl with an N50 value of 84.81 Mb (pseudochromosome-level assembly), and a high-confidence coding gene set to perform the genomic and evolutionary analyses of blue and green peafowls with 49 other avian species. The analyses revealed adaptive evolution of genes related to neuronal development, immunity, and skeletal muscle development in these peafowl species. Major genes related to axon guidance showed adaptive evolution in peafowl species. However, blue peafowl showed the presence of 42% more coding genes compared to the green peafowl along with a higher number of unique gene clusters, segmental duplicated genes and expanded gene families, and comparatively higher evolution in neuronal and developmental pathways. Blue peafowl also showed longer branch length compared to green peafowl in the species phylogenetic tree. These genomic insights obtained from the high-quality genome assembly ofP. cristatusconstructed in this study provide new clues on the superior adaptability of the blue peafowl over green peafowl despite having a recent species divergence time.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl

Chakraborty

Mondal

Mahajan

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…We mapped sequencing reads of 6 samples each from P. cristatus and P. muticus to the genome sequence of P. Muticus (Zhang et al 2022). The 2D-SFS between P. cristatus and P.…”

Section: (D) Population Genomic Summary Statisticsmentioning

confidence: 99%

“…Chromosome-level genome assemblies and genomic sampling of multiple individuals make this genus a compelling model for comparative genomics (Jaiswal et al 2018, Dong et al 2021, Zhang et al 2022. For instance, it allows us to compare the Z/A ratio between these species to get insights into mating system evolution.…”

Section: Introductionmentioning

confidence: 99%

Genome divergence across the Indo-Burman arc: a tale of two peacocks

Patil

Vijay

2022

Preprint

View full text Add to dashboard Cite

Exaggerated traits of the peacock are attributed to sexual selection. Yet, the two species of Asian peacock are conspicuously different in their plumage colouration and level of sexual dichromatism. Our integrative comparative study of bird calls, morphological differences and genomic divergence between the Indian blue peafowl and the green peafowl suggests a strong role of habitat differences in shaping species-specific changes. We estimate a recent (1-3 MYA) split of these species in the Pliocene or early Pleistocene, followed by intermittent periods of gene flow. Despite the relatively recent split, the high levels of genomic differentiation (FST ~ 0.6) mirror the divergence in morphological traits. Several genes involved in body patterning and colouration have accumulated protein-coding differences between the peacock species. Our estimates suggest genetic diversity in the widespread Indian peafowl (θw ~ 0.0015) is comparable but slightly higher than in the endangered green peafowl (θw ~ 0.0012). The ratio of genetic diversity on the Z chromosome to the autosomes (Z/A) is consistent with a polygynous mating system in the Indian peafowl compared to monogamy in the green peafowl. The Asian peacock species continue to provide exciting new insights into speciation and mating system evolution in the post-genomic era.

show abstract